Gen1 is 99-07, gen2 is 08-11. (Sorry to ramble, just unsure of which you have)Gen2 has a catalytic converter, gen1 does not. The converter is on the bottom of the header. Slip on mufflers will give you about 2 hp(you'll never notice the diffrence in power, you may notice the weight difference depending on what you have), and a full exhaust will give you around 10. These are just ballpark average numbers, every exhaust system and bike will vary. Slip ons are really just for looks, sound, and to save weight. It's easy to lose 10 to 15lbs off a gen2 with slip ons. Slip ons require no tuning, such as a power commander or better yet, the ECU Editor from site sponsor Boostbysmith.com(check it out, by far the best and cheapest way to tune a bike)
A full exhaust does not NEED any sort of tune either, the bike will not run lean or damage the engine in any way. However the bike will run much better with a tune. From what I've seen gen2 bikes seem to run better untuned than the gen1's do.
As far as a "tune" goes, you can have a basic fuel map for whatever exhaust you buy downloaded into your power commander. Boostbysmith offers all their previous made uploaded maps for free as well. These maps will make your bike run much better. The only way to get the bike to run at it's best is to have it tuned on a dynomometer, and by someone with a reputation that knows what they're doing. Depending on where you live, someone here can recommend a good tuner that is closest to you. Prices vary, but $250 to $400 seems average for the basic pipe/air filter tune. You will notice an improvement in hp, torque, and overall smoothness in idle and power delivery. A full exhaust, air filter, power commander/ecu editor with a dyno tune is well worth it if you can afford it.
If you like dual mufflers you can buy ANY brand you want and buy a Vance&Hines stainless steel header for $450. The V&H header works with ALL mufflers, including stock. It's available for gen1 or 2(the exhaust between the gen1 and 2 are different) and it doesn't have a catalytic converter. No full exhaust has a converter in it. The only full dual muffler exhaust as a complete system are Ti-Force, Brock's, and Akrapovic. The rest of the full systems are single muffler, and there are ALOT of different manufactures. Rule of thumb is that a full dual muffler system will make more low to midrange power as where a full single system will make more hp at high rpm's. The differnce though is minimal. The best thing you can do for exhaust is to look around at lots of them and pick out what YOU like the looks of best. Then find out how loud they are. Some are very quiet like stock and others are very loud. Sound clips on Youtube can't allow you to hear exactly what they really sound like either. A dragstrip is a good place to hear alot of them. Opinions on them vary, but there are lots of different setups on here. People will be glad to show you what they have.
I also gutted the catalytic converter on my gen2. It put out entirely too much heat and my feet are much cooler in the summer now.
If you have any questions, just ask. Most folks on here are glad to help. This is the best site to find out out anything Hayabusa.